Git & GitHub

 

Rodney Dyer, PhD

Git ?

Look Familiar?

What is Git

Git is a distributed versioning system

  • Easy for collaboration.
  • Easy track entire history of changes in your projects, documents, and code.
  • Complete history of all changes.
  • Easily revert to previous instances.
  • Project Based.
  • Branching

Lifetime of a Document

Consider a single file. After the first edit, you now have two differents ones.

graph LR
  A[File v1] -->|Edited| B[File v2]

In Google Docs, you can see the version history (and revert) while in Word you can use track changes to see edits but revisions are more complicated…

Persistence through Diffs

What we do not do is keep multiple versions of the file around as complete files. What is done is that the original document and only the changes made to the file—called diffs—are saved.

Lifetime of a Document

Add a new figure to the file and now you have three different entities.

graph LR
  A[File v1] -->|Edited| B[File v2]
  B -->|New Figure| C[File v3]

Lifetime of a Document

Perhaps the figure did not work out, and you decided to replace it with an image.

graph LR
  A[File v1] -->|Edited| B[File v2]
  B -->|Figure| C[File v3]
  B -->|Table| D[File v4]

For each new “revision”, you create a separate instance of the file itself.

Lifetime of a Document

Continue editing and making revisions.

graph LR
  A[File v1] -->|Edited| B[File v2]
  B -->|Figure| C[File v3]
  B -->|Table| D[File v4]
  D -->|Edited| E[File v5]

Lifetime of a Document

Eventually, you finish making revisions to the file.

graph LR
  A[File v1] -->|Edited| B[File v2]
  B -->|Figure| C[File v3]
  B -->|Table| D[File v4]
  D -->|Edited| E[File v5]
  E -->|Submitted| F[Thesis!]

Git allows you to have access to the entire history of the file and can revert to any of the previous version you want to.

Lifetime of a Document

Not all documents are incremental. Submitting for publication requires a different layout, citation format, etc. than for your thesis. Both of these are derived from File v5 as different branches.

graph LR
  A[File v1] -->|Edited| B[File v2]
  B -->|Figure| C[File v3]
  B -->|Table| D[File v4]
  D -->|Edited| E[File v5]
  E -->|Submitted| F[Thesis!]
  E -->|Submitted| G[Publication]

Git in Projects

This is a process that can include hundreds of files, data sets, images, shapefiles, etc. It is a Project Based approach.

And the entire project is referred to as a Repository.

Remote Locations

A git repository can live in many places.

  • On your laptop
  • On the lab computer
  • On a thumb drive (please do not use these any more)
  • On your home computer
  • On you iPhone

Synchronizing Repositories

Having a single remote Repository allows you to keep all the remote repositories in sync.

  1. Establish Repository on GitHub.
  2. Clone that repository to your local computer.
  3. Make changes.
  4. Commit changes when you are at a logical stoping point.
  5. PUSH the one or more committed changes to GitHub.
  6. On other computers with local copies, you PULL changes from GitHub to retrieve any changes you’ve made.

Pulling & Pushing.

For all these computers, you need to make sure you are pushing changes to GitHub from your current machine so that when you get to the next computer you can pull down these changes.

Collaborations

With a GitHub repository, several people can contribute to the same project and have access to the same content.

  • Can lead to conflicts
  • Merging files

The Profile Page

Github Repositories

  • history
  • files
  • description
  • settings
  • visibility
  • access

Access Controls

GitHub has a fine granularity of control over who can access content and how much access they can have.

  • Username + Password: Allows you to log into GitHub.
  • Access Control: Dictates who can see and check out repositories.
  • Username + Personal Access Token: Allow you to push content back to GitHub.

User Names & Passwords

If you are not using a password manager, PLEASE START TODAY.

  • 1Password
  • LastPass
  • mCrypt

Personal Access Tokens

Settings \(\to\) Developer Settings \(\to\) Personal Access Tokens

Scoped Tokens

Select custom length and allow for enough time to not be a problem. Save long token securely.

Creating a Repository

From your profile page, select the Repositories menu and follow the instructions.
- Names & Descriptions.
- Private vs Public.
- The README.md file as your ‘front page’.
- The .gitignore file.
- Licenses.
- Websites.

Online Editing

The repository interface allows:

  • Adding and deleting of files.
  • Editing file content.
  • Deploying to websites.
  • Wiki/Comments/Feedback.

Going Forward

 

Questions

 

If you have any questions, please feel free to either post to the Canvas discussion board for the class or drop me an email.

Peter Sellers looking bored

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